[InterMine Dev] Error on web app deployment

Paulo Nuin paulo.nuin at gmail.com
Tue Aug 4 23:02:17 BST 2015


Hi Julie

We are still trying to determine what has been changed in our code base to try to trace the problem. We are not discarding a merge problem, but the deployment was working fine before some modifications were performed, but project.properties was not a part of the modifications. Changing it to a similar content to 

https://github.com/intermine/intermine/blob/beta/intermine/objectstore/main/project.properties

brought us to another error:

-load-int-tasks:
     [echo] Loading integration tasks
     [null] Exiting /mnt/data/intermine/intermine/api/model/userprofile/build.xml.

BUILD FAILED
/mnt/data/intermine/imbuild/library.xml:78: The following error occurred while executing this line:
/mnt/data/intermine/imbuild/task.xml:146: The following error occurred while executing this line:
Unable to find jar:file:/mnt/data/intermine/intermine/integrate/main/dist/intermine-integrate.jar!/org/intermine/task/antlib-int.xml
	at org.apache.tools.ant.taskdefs.Antlib.createAntlib(Antlib.java:68)
	at org.apache.tools.ant.taskdefs.Definer.loadAntlib(Definer.java:440)
	at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:292)
	at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
	at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:606)
	at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
	at org.apache.tools.ant.Task.perform(Task.java:348)
	at org.apache.tools.ant.Target.execute(Target.java:392)
	at org.apache.tools.ant.Target.performTasks(Target.java:413)
	at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1399)
	at org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
	at org.apache.tools.ant.Project.executeTargets(Project.java:1251)
	at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:442)
	at org.intermine.task.Dependencies.execute(Dependencies.java:304)
	at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
	at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:606)
	at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
	at org.apache.tools.ant.Task.perform(Task.java:348)
	at org.apache.tools.ant.Target.execute(Target.java:392)
	at org.apache.tools.ant.Target.performTasks(Target.java:413)
	at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1399)
	at org.apache.tools.ant.Project.executeTarget(Project.java:1368)
	at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
	at org.apache.tools.ant.Project.executeTargets(Project.java:1251)
	at org.apache.tools.ant.Main.runBuild(Main.java:811)
	at org.apache.tools.ant.Main.startAnt(Main.java:217)
	at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
	at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
Caused by: java.io.FileNotFoundException: JAR entry org/intermine/task/antlib-int.xml not found in /mnt/data/intermine/intermine/integrate/main/dist/intermine-integrate.jar
	at sun.net.www.protocol.jar.JarURLConnection.connect(JarURLConnection.java:140)
	at org.apache.tools.ant.taskdefs.Antlib.createAntlib(Antlib.java:66)
	... 31 more

Again, we am checking everything on our end for possible causes.

thanks a lot

Paulo



> On Aug 3, 2015, at 2:07 AM, Julie Sullivan <julie at flymine.org> wrote:
> 
> Hi Paulo
> 
> You seem to be having trouble finding the AttributeDescriptor object.
> 
> Here I see your file contains no dependencies for the objectstore project:
> 
> https://github.com/WormBase/intermine/blob/dev/intermine/objectstore/main/project.properties
> 
> Compared with the InterMine file which has a dependency on the Model project, where the "AttributeDescriptor" class lives.
> 
> https://github.com/intermine/intermine/blob/beta/intermine/objectstore/main/project.properties
> 
> It would make sense that you are having issues if your dependencies are wrong. Do you know how this might have happened? Why your file is different?
> 
> This change was done in April 2014 so it was part of InterMine 1.4.
> 
> I assume you are using InterMine 1.4? Maybe you had a merging problem? Or need to do a clean? Can you look at the project properties file for the objectstore project (the project that is generating the error below), and confirm it does depend on the model project?
> 
> Let me know what you find!
> Julie
> 
> 
> On 03/08/15 07:56, Paulo Nuin wrote:
>> Hi
>> 
>> In our attempt to have an updated version of WormMine, we are having
>> trouble deploying the Tomcat web app. The error happens on some javac
>> compilation steps:
>> 
>> [dependencies] warning: [options] bootstrap class path not set in
>> conjunction with -source 1.6
>> [dependencies]
>> /mnt/data/intermine/intermine/objectstore/main/src/org/intermine/codegen/JavaModelOutput.java:512:
>> error: cannot find symbol
>> [dependencies] if (attr.isPrimitive() || attr.isNumeric()) {
>> [dependencies]                              ^
>> [dependencies]   symbol:   method isNumeric()
>> [dependencies]   location: variable attr of type AttributeDescriptor
>> [dependencies]
>> /mnt/data/intermine/intermine/objectstore/main/src/org/intermine/modelproduction/ModelMerger.java:95:
>> error: cannot find symbol
>> [dependencies]                     original.getVersion(), new
>> HashSet<ClassDescriptor>(newClasses.values()));
>> [dependencies]                             ^
>> [dependencies]   symbol:   method getVersion()
>> [dependencies]   location: variable original of type Model
>> [dependencies] Note:
>> /mnt/data/intermine/intermine/objectstore/main/src/org/intermine/objectstore/query/QueryField.java
>> uses or overrides a deprecated API.
>> [dependencies] Note: Recompile with -Xlint:deprecation for details.
>> [dependencies] Note: Some input files use unchecked or unsafe operations.
>> [dependencies] Note: Recompile with -Xlint:unchecked for details.
>> [dependencies] 2 errors
>> [dependencies] 1 warning
>>      [null] Exiting
>> /mnt/data/intermine/intermine/objectstore/main/build.xml.
>> 
>> 
>> The problems seem to be in attire.isNumeric and original.getVersion().
>> 
>> Any help is appreciated.
>> 
>> Thanks
>> 
>> Paulo
>> 




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